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- <?php
- /**
- * @file
- * Contains functions for the Materialized Views API
- * @defgroup tripal_mviews_api Core Module Materalized Views API
- * @{
- * Provides an application programming interface (API) to manage materialized views in Chado.
- * The Perl-based chado comes with an interface for managing materialzed views. This
- * API provides an alternative Drupal-based method.
- * @}
- * @ingroup tripal_api
- */
- /**
- * Add a materialized view to the chado database to help speed data access. This
- * function supports the older style where postgres column specifications
- * are provided using the $mv_table, $mv_specs and $indexed variables. It also
- * supports the newer preferred method where the materialized view is described
- * using the Drupal Schema API array.
- *
- * @param $name
- * The name of the materialized view.
- * @param $modulename
- * The name of the module submitting the materialized view (e.g. 'tripal_library')
- * @param $mv_table
- * The name of the table to add to chado. This is the table that can be queried.
- * @param $mv_specs
- * The table definition
- * @param $indexed
- * The columns that are to be indexed
- * @param $query
- * The SQL query that loads the materialized view with data
- * @param $special_index
- * currently not used
- * @param $comment
- * A string containing a description of the materialized view
- * @param $mv_schema
- * If using the newer Schema API array to define the materialized view then
- * this variable should contain the array or a string representation of the
- * array.
- *
- * @ingroup tripal_mviews_api
- */
- function tripal_add_mview($name, $modulename, $mv_table, $mv_specs, $indexed,
- $query, $special_index, $comment = NULL, $mv_schema = NULL) {
- // get the table name from the schema array
- $schema_arr = array();
- if ($mv_schema) {
- // if the schema is provided as a string then convert it to an array
- if (!is_array($mv_schema)) {
- eval("\$schema_arr = $mv_schema;");
- }
- // if the schema is provided as an array then create a string
- // copy of it for storage in the mview
- else {
- $schema_arr = $mv_schema;
- $mv_schema = var_export($schema_arr, 1);
- }
- $mv_table = $schema_arr['table'];
- }
- // Create a new record
- $record = new stdClass();
- $record->name = $name;
- $record->modulename = $modulename;
- $record->mv_table = $mv_table;
- $record->mv_specs = $mv_specs;
- $record->indexed = $indexed;
- $record->query = $query;
- $record->special_index = $special_index;
- $record->comment = $comment;
- $record->mv_schema = $mv_schema;
- // add the record to the tripal_mviews table and if successful
- // create the new materialized view in the chado schema
- if (drupal_write_record('tripal_mviews', $record)) {
- // drop the table from chado if it exists
- $previous_db = tripal_db_set_active('chado'); // use chado database
- if (db_table_exists($mv_table)) {
- $sql = "DROP TABLE $mv_table";
- db_query($sql);
- }
- tripal_db_set_active($previous_db); // now use drupal database
- // now construct the indexes
- $index = '';
- if ($indexed) {
- // add to the array of values
- $vals = preg_split("/[\n,]+/", $indexed);
- $index = '';
- foreach ($vals as $field) {
- $field = trim($field);
- $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
- }
- }
- // create the table differently depending on if it the traditional method
- // or the Drupal Schema API method
- if ($mv_schema) {
- if (!tripal_core_create_custom_table ($ret, $mv_table, $schema_arr, 0)) {
- drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."), 'error');
- }
- else {
- drupal_set_message(t("View '%name' created", array('%name' => $name)));
- }
- }
- else {
- // add the table to the database
- $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index";
- $previous_db = tripal_db_set_active('chado'); // use chado database
- $results = db_query($sql);
- tripal_db_set_active($previous_db); // now use drupal database
- if ($results) {
- drupal_set_message(t("View '%name' created", array('%name' => $name)));
- }
- else {
- drupal_set_message(t("Failed to create the materialized view table: '%mv_table'", array('%mv_table' => $mv_table)), 'error');
- }
- }
- }
- }
- /**
- * Edits a materialized view to the chado database to help speed data access.This
- * function supports the older style where postgres column specifications
- * are provided using the $mv_table, $mv_specs and $indexed variables. It also
- * supports the newer preferred method where the materialized view is described
- * using the Drupal Schema API array.
- *
- * @param $mview_id
- * The mview_id of the materialized view to edit
- * @param $name
- * The name of the materialized view.
- * @param $modulename
- * The name of the module submitting the materialized view (e.g. 'tripal_library')
- * @param $mv_table
- * The name of the table to add to chado. This is the table that can be queried.
- * @param $mv_specs
- * The table definition
- * @param $indexed
- * The columns that are to be indexed
- * @param $query
- * The SQL query that loads the materialized view with data
- * @param $special_index
- * currently not used
- * @param $comment
- * A string containing a description of the materialized view
- * @param $mv_schema
- * If using the newer Schema API array to define the materialized view then
- * this variable should contain the array.
- *
- * @ingroup tripal_mviews_api
- */
- function tripal_edit_mview($mview_id, $name, $modulename, $mv_table, $mv_specs,
- $indexed, $query, $special_index, $comment = NULL, $mv_schema = NULL) {
- // get the table name from the schema array
- $schema_arr = array();
- if ($mv_schema) {
- // get the schema from the mv_specs and use it to add the custom table
- eval("\$schema_arr = $mv_schema;");
- $mv_table = $schema_arr['table'];
- }
- // Create a new record
- $record = new stdClass();
- $record->mview_id = $mview_id;
- $record->name = $name;
- $record->modulename = $modulename;
- $record->mv_schema = $mv_schema;
- $record->mv_table = $mv_table;
- $record->mv_specs = $mv_specs;
- $record->indexed = $indexed;
- $record->query = $query;
- $record->special_index = $special_index;
- $record->last_update = 0;
- $record->status = '';
- $record->comment = $comment;
- // drop the table from chado if it exists
- $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d";
- $mview = db_fetch_object(db_query($sql, $mview_id));
- $previous_db = tripal_db_set_active('chado'); // use chado database
- if (db_table_exists($mview->mv_table)) {
- $sql = "DROP TABLE %s";
- db_query($sql, $mview->mv_table);
- }
- tripal_db_set_active($previous_db); // now use drupal database
- // update the record to the tripal_mviews table and if successful
- // create the new materialized view in the chado schema
- if (drupal_write_record('tripal_mviews', $record, 'mview_id')) {
- // drop the table from chado if it exists
- $previous_db = tripal_db_set_active('chado'); // use chado database
- if (db_table_exists($mv_table)) {
- $sql = "DROP TABLE %s";
- db_query($sql, $mv_table);
- }
- tripal_db_set_active($previous_db); // now use drupal database
- // now construct the indexes
- $index = '';
- if ($indexed) {
- // add to the array of values
- $vals = preg_split("/[\n,]+/", $indexed);
- $index = '';
- foreach ($vals as $field) {
- $field = trim($field);
- $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
- }
- }
- // re-create the table differently depending on if it the traditional method
- // or the Drupal Schema API method
- if ($mv_schema) {
- if (!tripal_core_create_custom_table($ret, $mv_table, $schema_arr, 0)) {
- drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."));
- }
- else {
- drupal_set_message(t("View '%name' created", array('%name' => $name)));
- }
- }
- else {
- $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index";
- $previous_db = tripal_db_set_active('chado'); // use chado database
- $results = db_query($sql);
- tripal_db_set_active($previous_db); // now use drupal database
- if ($results) {
- drupal_set_message(t("View '%name' edited and saved. All results cleared. Please re-populate the view.", array('%name' => $name)));
- }
- else {
- drupal_set_message(t("Failed to create the materialized view table: '%mv_table'", array('%mv_table' => $mv_table)), 'error');
- }
- }
- }
- }
- /**
- * Retrieve the materialized view_id given the name
- *
- * @param $view_name
- * The name of the materialized view
- *
- * @return
- * The unique identifier for the given view
- *
- * @ingroup tripal_mviews_api
- */
- function tripal_mviews_get_mview_id($view_name) {
- $sql = "SELECT * FROM {tripal_mviews} ".
- "WHERE name = '%s'";
- if (db_table_exists('tripal_mviews')) {
- $mview = db_fetch_object(db_query($sql, $view_name));
- if ($mview) {
- return $mview->mview_id;
- }
- }
- return FALSE;
- }
- /**
- * Does the specified action for the specified Materialized View
- *
- * @param $op
- * The action to be taken. One of update or delete
- * @param $mview_id
- * The unique ID of the materialized view for the action to be performed on
- * @param $redirect
- * TRUE/FALSE depending on whether you want to redirect the user to admin/tripal/mviews
- *
- * @ingroup tripal_core
- */
- function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
- global $user;
- $args = array("$mview_id");
- if (!$mview_id) {
- return '';
- }
- // get this mview details
- $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d";
- $mview = db_fetch_object(db_query($sql, $mview_id));
- // add a job or perform the action based on the given operation
- if ($op == 'update') {
- tripal_add_job("Populate materialized view '$mview->name'", 'tripal_core',
- 'tripal_update_mview', $args, $user->uid);
- }
- if ($op == 'delete') {
- // remove the mview from the tripal_mviews table
- $sql = "DELETE FROM {tripal_mviews} ".
- "WHERE mview_id = $mview_id";
- db_query($sql);
- // drop the table from chado if it exists
- $previous_db = tripal_db_set_active('chado'); // use chado database
- if (db_table_exists($mview->mv_table)) {
- $sql = "DROP TABLE $mview->mv_table";
- db_query($sql);
- }
- tripal_db_set_active($previous_db); // now use drupal database
- }
- // Redirect the user
- if ($redirect) {
- drupal_goto("admin/tripal/mviews");
- }
- }
- /**
- * Update a Materialized View
- *
- * @param $mview_id
- * The unique identifier for the materialized view to be updated
- *
- * @return
- * True if successful, FALSE otherwise
- *
- * @ingroup tripal_mviews_api
- */
- function tripal_update_mview($mview_id) {
- $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d ";
- $mview = db_fetch_object(db_query($sql, $mview_id));
- if ($mview) {
- $previous_db = tripal_db_set_active('chado'); // use chado database
- $results = db_query("DELETE FROM {%s}", $mview->mv_table);
- $results = db_query("INSERT INTO {%s} ($mview->query)", $mview->mv_table);
- tripal_db_set_active($previous_db); // now use drupal database
- if ($results) {
- $sql = "SELECT count(*) as cnt FROM {%s}";
- $previous_db = tripal_db_set_active('chado'); // use chado database
- $count = db_fetch_object(db_query($sql, $mview->mv_table));
- tripal_db_set_active($previous_db); // now use drupal database
- $record = new stdClass();
- $record->mview_id = $mview_id;
- $record->last_update = time();
- $record->status = "Populated with " . number_format($count->cnt) . " rows";
- drupal_write_record('tripal_mviews', $record, 'mview_id');
- return TRUE;
- }
- else {
- // print and save the error message
- $record = new stdClass();
- $record->mview_id = $mview_id;
- $record->status = "ERROR populating. See Drupal's recent log entries for details.";
- print $record->status . "\n";
- drupal_write_record('tripal_mviews', $record, 'mview_id');
- return FALSE;
- }
- }
- }
- /**
- * A template function which returns markup to display details for the current materialized view
- *
- * @param $mview_id
- * The unique ID of the materialized view to render
- *
- * @ingroup tripal_mviews_api
- */
- function tripal_mview_report($mview_id) {
- // get this mview details
- $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d";
- $mview = db_fetch_object(db_query($sql, $mview_id));
- // create a table with each row containig stats for
- // an individual job in the results set.
- $return_url = url("admin/tripal/mviews/");
- $output .= "<p><a href=\"$return_url\">Return to table of materialized views.</a></p>";
- $output .= "<br />";
- $output .= "<p>Details for <b>$mview->name</b>:</p>";
- $output .= "<br />";
- $output .= "<table class=\"border-table\">";
- if ($mview->name) {
- $output .= " <tr>".
- " <th>View Name</th>".
- " <td>$mview->name</td>".
- " </tr>";
- }
- if ($mview->modulename) {
- $output .= " <tr>".
- " <th>Module Name</th>".
- " <td>$mview->modulename</td>".
- " </tr>";
- }
- if ($mview->mv_table) {
- $output .= " <tr>".
- " <th>Table Name</th>".
- " <td>$mview->mv_table</td>".
- " </tr>";
- }
- if ($mview->mv_specs) {
- $output .= " <tr>".
- " <th>Table Field Definitions</th>".
- " <td>$mview->mv_specs</td>".
- " </tr>";
- }
- if ($mview->query) {
- $output .= " <tr>".
- " <th>Query</th>".
- " <td><pre>$mview->query</pre></td>".
- " </tr>";
- }
- if ($mview->indexed) {
- $output .= " <tr>".
- " <th>Indexed Fields</th>".
- " <td>$mview->indexed</td>".
- " </tr>";
- }
- if ($mview->special_index) {
- $output .= " <tr>".
- " <th>Special Indexed Fields</th>".
- " <td>$mview->speical_index</td>".
- " </tr>";
- }
- if ($mview->last_update > 0) {
- $update = format_date($mview->last_update);
- }
- else {
- $update = 'Not yet populated';
- }
- $output .= " <tr>".
- " <th>Last Update</th>".
- " <td>$update</td>".
- " </tr>";
- // build the URLs using the url function so we can handle installations where
- // clean URLs are or are not used
- $update_url = url("admin/tripal/mviews/action/update/$mview->mview_id");
- $delete_url = url("admin/tripal/mviews/action/delete/$mview->mview_id");
- $edit_url = url("admin/tripal/mviews/edit/$mview->mview_id");
- $output .= "<tr><th>Actions</th>".
- "<td> <a href='$update_url'>Populate</a>, ".
- " <a href='$edit_url'>Edit</a>, ".
- " <a href='$delete_url'>Delete</a></td></tr>";
- $output .= "</table>";
- return $output;
- }
- /**
- * A template function to render a listing of all Materialized Views
- *
- * @ingroup tripal_mviews_api
- */
- function tripal_mviews_report() {
- $header = array('', 'MView Name', 'Last Update', 'Status', 'Description', '');
- $rows = array();
- $mviews = db_query("SELECT * FROM {tripal_mviews} ORDER BY name");
- while ($mview = db_fetch_object($mviews)) {
- if ($mview->last_update > 0) {
- $update = format_date($mview->last_update);
- }
- else {
- $update = 'Not yet populated';
- }
- $rows[] = array(
- l(t('View'), "admin/tripal/mviews/report/$mview->mview_id") ." | ".
- l(t('Edit'), "admin/tripal/mviews/edit/$mview->mview_id") ." | ".
- l(t('Populate'), "admin/tripal/mviews/action/update/$mview->mview_id"),
- $mview->name,
- $update,
- $mview->status,
- $mview->comment,
- l(t('Delete'), "admin/tripal/mviews/action/delete/$mview->mview_id"),
- );
- }
- $rows[] = array(
- 'data' => array(
- array('data' => l(t('Create a new materialized view.'), "admin/tripal/mviews/new"),
- 'colspan' => 6),
- )
- );
- $page = theme('table', $header, $rows);
- return $page;
- }
- /**
- * A Form to Create/Edit a Materialized View
- *
- * @param $form_state
- * The current state of the form (Form API)
- * @param $mview_id
- * The unique ID of the Materialized View to Edit or NULL if creating a new materialized view
- *
- * @return
- * A form array (Form API)
- *
- * @ingroup tripal_core
- */
- function tripal_mviews_form(&$form_state = NULL, $mview_id = NULL) {
- if (!$mview_id) {
- $action = 'Add';
- }
- else {
- $action = 'Edit';
- }
- // get this requested view
- if (strcmp($action, 'Edit')==0) {
- $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = %d ";
- $mview = db_fetch_object(db_query($sql, $mview_id));
- // set the default values. If there is a value set in the
- // form_state then let's use that, otherwise, we'll pull
- // the values from the database
- $default_name = $form_state['values']['name'];
- $default_mv_table = $form_state['values']['mv_table'];
- $default_mv_specs = $form_state['values']['mv_specs'];
- $default_indexed = $form_state['values']['indexed'];
- $default_mvquery = $form_state['values']['mvquery'];
- $default_special_index = $form_state['values']['special_index'];
- $default_comment = $form_state['values']['cpmment'];
- if (!$default_name) {
- $default_name = $mview->name;
- }
- if (!$default_mv_table) {
- $default_mv_table = $mview->mv_table;
- }
- if (!$default_mv_specs) {
- $default_mv_specs = $mview->mv_specs;
- }
- if (!$default_indexed) {
- $default_indexed = $mview->indexed;
- }
- if (!$default_mvquery) {
- $default_mvquery = $mview->query;
- }
- if (!$default_special_index) {
- $default_special_index = $mview->special_index;
- }
- if (!$default_comment) {
- $default_comment = $mview->comment;
- }
- if (!$default_schema) {
- $default_schema = $mview->mv_schema;
- }
- // the mv_table column of the tripal_mviews table always has the table
- // name even if it is a custom table. However, for the sake of the form,
- // we do not want this to show up as the mv_table is needed for the
- // traditional style input. We'll blank it out if we have a custom
- // table and it will get reset in the submit function using the
- // 'table' value from the schema array
- if ($default_schema) {
- $default_mv_table = '';
- }
- // set which fieldset is collapsed
- $schema_collapsed = 0;
- $traditional_collapsed = 1;
- if (!$default_schema) {
- $schema_collapsed = 1;
- $traditional_collapsed = 0;
- }
- }
- // Build the form
- $form['action'] = array(
- '#type' => 'value',
- '#value' => $action
- );
- $form['mview_id'] = array(
- '#type' => 'value',
- '#value' => $mview_id
- );
- $form['name']= array(
- '#type' => 'textfield',
- '#title' => t('View Name'),
- '#description' => t('Please enter the name for this materialized view.'),
- '#required' => TRUE,
- '#default_value' => $default_name,
- );
- $form['comment']= array(
- '#type' => 'textarea',
- '#title' => t('MView Description'),
- '#description' => t('Optional. Please provide a description of the purpose for this materialized vieww.'),
- '#required' => FALSE,
- '#default_value' => $default_comment,
- );
- // add a fieldset for the Drupal Schema API
- $form['schema'] = array(
- '#type' => 'fieldset',
- '#title' => 'Drupal Schema API Setup',
- '#description' => t('Use the Drupal Schema API array to describe a table. The benefit is that it '.
- 'can be fully integrated with Tripal Views. Tripal supports an extended '.
- 'array format to allow for descriptoin of foreign key relationships.'),
- '#collapsible' => 1,
- '#collapsed' => $schema_collapsed ,
- );
- $form['schema']['schema']= array(
- '#type' => 'textarea',
- '#title' => t('Schema Array'),
- '#description' => t('Please enter the Drupal Schema API compatible array that defines the table.'),
- '#required' => FALSE,
- '#default_value' => $default_schema,
- '#rows' => 25,
- );
- // add a fieldset for the Original Table Description fields
- $form['traditional'] = array(
- '#type' => 'fieldset',
- '#title' => 'Traditional MViews Setup',
- '#description' => t('Traidtionally with Tripal MViews were created by specifying PostgreSQL style '.
- 'column types. This method can be used but is deprecated in favor of the '.
- 'newer Drupal schema API method provided above.'),
- '#collapsible' => 1,
- '#collapsed' => $traditional_collapsed,
- );
- $form['traditional']['mv_table']= array(
- '#type' => 'textfield',
- '#title' => t('Table Name'),
- '#description' => t('Please enter the table name that this view will generate in the database. You can use the schema and table name for querying the view'),
- '#required' => FALSE,
- '#default_value' => $default_mv_table,
- );
- $form['traditional']['mv_specs']= array(
- '#type' => 'textarea',
- '#title' => t('Table Definition'),
- '#description' => t('Please enter the field definitions for this view. Each field should be separated by a comma or enter each field definition on each line.'),
- '#required' => FALSE,
- '#default_value' => $default_mv_specs,
- );
- $form['traditional']['indexed']= array(
- '#type' => 'textarea',
- '#title' => t('Indexed Fields'),
- '#description' => t('Please enter the field names (as provided in the table definition above) that will be indexed for this view. Separate by a comma or enter each field on a new line.'),
- '#required' => FALSE,
- '#default_value' => $default_indexed,
- );
- /**
- $form['traditional']['special_index']= array(
- '#type' => 'textarea',
- '#title' => t('View Name'),
- '#description' => t('Please enter the name for this materialized view.'),
- '#required' => TRUE,
- '#default_value' => $default_special_index,
- );
- */
- $form['mvquery']= array(
- '#type' => 'textarea',
- '#title' => t('Query'),
- '#description' => t('Please enter the SQL statement used to populate the table.'),
- '#required' => TRUE,
- '#default_value' => $default_mvquery,
- '#rows' => 25,
- );
- if ($action == 'Edit') {
- $value = 'Save';
- }
- if ($action == 'Add') {
- $value = 'Add';
- }
- $form['submit'] = array(
- '#type' => 'submit',
- '#value' => t($value),
- '#weight' => 9,
- '#executes_submit_callback' => TRUE,
- );
- $form['#redirect'] = 'admin/tripal/mviews';
- return $form;
- }
- /**
- * Validate the Create/Edit Materialized View Form
- * Implements hook_form_validate().
- *
- * @ingroup tripal_core
- */
- function tripal_mviews_form_validate($form, &$form_state) {
- $action = $form_state['values']['action'];
- $mview_id = $form_state['values']['mview_id'];
- $name = $form_state['values']['name'];
- $mv_table = $form_state['values']['mv_table'];
- $mv_specs = $form_state['values']['mv_specs'];
- $indexed = $form_state['values']['indexed'];
- $query = $form_state['values']['mvquery'];
- $special_index = $form_state['values']['special_index'];
- $comment = $form_state['values']['comment'];
- $schema = $form_state['values']['schema'];
- if ($schema and ($mv_table or $mv_specs or $indexed or $special_index)) {
- form_set_error($form_state['values']['schema'],
- t('You can create an MView using the Drupal Schema API method or the '.
- 'traditional method but not both.'));
- }
- if (!$schema) {
- if (!$mv_specs) {
- form_set_error($form_state['values']['mv_specs'],
- t('The Table Definition field is required.'));
- }
- if (!$mv_table) {
- form_set_error($form_state['values']['mv_table'],
- t('The Table Name field is required.'));
- }
- }
- // make sure the array is valid
- if ($schema) {
- $success = eval("\$schema_array = $schema;");
- if ($success === FALSE) {
- $error = error_get_last();
- form_set_error($form_state['values']['schema'],
- t("The schema array is improperly formatted. Parse Error : " . $error["message"]));
- }
- if (!array_key_exists('table', $schema_array)) {
- form_set_error($form_state['values']['schema'],
- t("The schema array must have key named 'table'"));
- }
- // TODO: add in more validation checks of the array to help the user
- }
- }
- /**
- * Submit the Create/Edit Materialized View Form
- * Implements hook_form_submit().
- *
- * @ingroup tripal_core
- */
- function tripal_mviews_form_submit($form, &$form_state) {
- $ret = array();
- $action = $form_state['values']['action'];
- $mview_id = $form_state['values']['mview_id'];
- $name = $form_state['values']['name'];
- $mv_table = $form_state['values']['mv_table'];
- $mv_specs = $form_state['values']['mv_specs'];
- $indexed = $form_state['values']['indexed'];
- $query = $form_state['values']['mvquery'];
- $special_index = $form_state['values']['special_index'];
- $comment = $form_state['values']['comment'];
- $schema = $form_state['values']['schema'];
- if (strcmp($action, 'Edit') == 0) {
- tripal_edit_mview($mview_id, $name, 'tripal_core', $mv_table, $mv_specs,
- $indexed, $query, $special_index, $comment, $schema);
- }
- elseif (strcmp($action, 'Add') == 0) {
- tripal_add_mview($name, 'tripal_core', $mv_table, $mv_specs,
- $indexed, $query, $special_index, $comment, $schema);
- }
- else {
- drupal_set_message(t("No action performed."));
- }
- return '';
- }
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